---
title: "COVID-19 Pandemic"
output:
flexdashboard::flex_dashboard:
orientation: rows
social: menu
source_code: embed
---
```{r setup, include=FALSE}
library(dygraphs)
library(xts)
library(lubridate)
library(dplyr)
library(tidyr)
### Data sources:
### Our World In Data https://ourworldindata.org/coronavirus
### Johns Hopkins Coronavirus Resource Center https://github.com/govex/COVID-19/tree/master/data_tables/vaccine_data/global_data
covid <- read.csv(url("https://raw.githubusercontent.com/owid/covid-19-data/master/public/data/owid-covid-data.csv"))
uk_covid <- covid %>%
filter(location == "United Kingdom")
hun_covid <- covid %>%
filter(location == "Hungary")
vax <- read.csv(url("https://raw.githubusercontent.com/govex/COVID-19/master/data_tables/vaccine_data/global_data/time_series_covid19_vaccine_global.csv"))
hun_vax <- vax %>%
filter(Country_Region == "Hungary")
```
United Kingdom
=======================================================================
Row
-----------------------------------------------------------------------
### New cases
```{r, include=FALSE}
uk_covid_sub <- subset(uk_covid, select = -c(1:3, 5, 7:59))
uk_covid_sub$date <- ymd(uk_covid_sub$date)
str(uk_covid_sub)
data <- xts(x = uk_covid_sub$new_cases, order.by = uk_covid_sub$date)
names(data) <- c("New cases")
data <- abs(data$`New cases`)
```
```{r}
dygraph(data) %>%
dyOptions(fillGraph = TRUE, fillAlpha = 0.5, colors = "#337ab7") %>%
dyCrosshair(direction = "vertical") %>%
dyLegend(show = "always") %>%
dyEvent("2021-05-11", "Delta (VOC)", labelLoc = "bottom") %>%
dyEvent("2021-11-26", "Omicron (VOC)", labelLoc = "bottom") %>%
dyRangeSelector()
```
### New tests
```{r, include=FALSE}
uk_covid_sub <- subset(uk_covid, select = -c(1:3, 5, 27:59))
uk_covid_sub$date <- ymd(uk_covid_sub$date)
str(uk_covid_sub)
data <- xts(x = uk_covid_sub$new_tests, order.by = uk_covid_sub$date)
names(data) <- c("New tests")
```
```{r}
dygraph(data) %>%
dyOptions(fillGraph = TRUE, fillAlpha = 0.5, colors = "#337ab7") %>%
dyCrosshair(direction = "vertical") %>%
dyLegend(show = "always") %>%
dyEvent("2021-05-11", "Delta (VOC)", labelLoc = "bottom") %>%
dyEvent("2021-11-26", "Omicron (VOC)", labelLoc = "bottom") %>%
dyRangeSelector()
```
Row
-----------------------------------------------------------------------
### Hospital patients
```{r, include=FALSE}
uk_covid_sub <- subset(uk_covid, select = -c(1:3, 5, 21:59))
uk_covid_sub$date <- ymd(uk_covid_sub$date)
str(uk_covid_sub)
data <- xts(x = uk_covid_sub$hosp_patients, order.by = uk_covid_sub$date)
names(data) <- c("Hospital patients")
```
```{r}
dygraph(data) %>%
dyOptions(fillGraph = TRUE, fillAlpha = 0.5, colors = "#337ab7") %>%
dyCrosshair(direction = "vertical") %>%
dyLegend(show = "always") %>%
dyEvent("2021-05-11", "Delta (VOC)", labelLoc = "bottom") %>%
dyEvent("2021-11-26", "Omicron (VOC)", labelLoc = "bottom") %>%
dyRangeSelector()
```
### ICU patients
```{r, include=FALSE}
uk_covid_sub <- subset(uk_covid, select = -c(1:3, 5, 19:59))
uk_covid_sub$date <- ymd(uk_covid_sub$date)
str(uk_covid_sub)
data <- xts(x = uk_covid_sub$icu_patients, order.by = uk_covid_sub$date)
names(data) <- c("ICU patients")
```
```{r}
dygraph(data) %>%
dyOptions(fillGraph = TRUE, fillAlpha = 0.5, colors = "#337ab7") %>%
dyCrosshair(direction = "vertical") %>%
dyLegend(show = "always") %>%
dyEvent("2021-05-11", "Delta (VOC)", labelLoc = "bottom") %>%
dyEvent("2021-11-26", "Omicron (VOC)", labelLoc = "bottom") %>%
dyRangeSelector()
```
### New deaths
```{r, include=FALSE}
uk_covid_sub <- subset(uk_covid, select = -c(1:3, 5, 10:59))
uk_covid_sub$date <- ymd(uk_covid_sub$date)
str(uk_covid_sub)
data <- xts(x = uk_covid_sub$new_deaths, order.by = uk_covid_sub$date)
names(data) <- c("New deaths")
```
```{r}
dygraph(data) %>%
dyOptions(fillGraph = TRUE, fillAlpha = 0.5, colors = "#337ab7") %>%
dyCrosshair(direction = "vertical") %>%
dyLegend(show = "always") %>%
dyEvent("2021-05-11", "Delta (VOC)", labelLoc = "bottom") %>%
dyEvent("2021-11-26", "Omicron (VOC)", labelLoc = "bottom") %>%
dyRangeSelector()
```
### New deaths per million
```{r, include=FALSE}
uk_covid_sub <- subset(uk_covid, select = -c(1:3, 5, 16:59))
uk_covid_sub$date <- ymd(uk_covid_sub$date)
str(uk_covid_sub)
data <- xts(x = uk_covid_sub$new_deaths_per_million, order.by = uk_covid_sub$date)
names(data) <- c("New deaths per million")
```
```{r}
dygraph(data) %>%
dyOptions(fillGraph = TRUE, fillAlpha = 0.5, colors = "#337ab7") %>%
dyCrosshair(direction = "vertical") %>%
dyLegend(show = "always") %>%
dyEvent("2021-05-11", "Delta (VOC)", labelLoc = "bottom") %>%
dyEvent("2021-11-26", "Omicron (VOC)", labelLoc = "bottom") %>%
dyRangeSelector()
```
Row
-----------------------------------------------------------------------
### People partially vaccinated (1st dose)
```{r, include=FALSE}
uk_covid_sub <- subset(uk_covid, select = -c(1:3, 5, 40:59))
uk_covid_sub$date <- ymd(uk_covid_sub$date)
str(uk_covid_sub)
data <- xts(x = uk_covid_sub$people_vaccinated, order.by = uk_covid_sub$date)
names(data) <- c("People partially vaccinated")
```
```{r}
dygraph(data) %>%
dyOptions(fillGraph = TRUE, fillAlpha = 0.5, colors = "#337ab7") %>%
dyCrosshair(direction = "vertical") %>%
dyLegend(show = "always") %>%
dyEvent("2021-05-11", "Delta (VOC)", labelLoc = "bottom") %>%
dyEvent("2021-11-26", "Omicron (VOC)", labelLoc = "bottom") %>%
dyRangeSelector()
```
### People fully vaccinated (2nd dose)
```{r, include=FALSE}
uk_covid_sub <- subset(uk_covid, select = -c(1:3, 5, 40:59))
uk_covid_sub$date <- ymd(uk_covid_sub$date)
str(uk_covid_sub)
data <- xts(x = uk_covid_sub$people_fully_vaccinated, order.by = uk_covid_sub$date)
names(data) <- c("People fully vaccinated")
```
```{r}
dygraph(data) %>%
dyOptions(fillGraph = TRUE, fillAlpha = 0.5, colors = "#337ab7") %>%
dyCrosshair(direction = "vertical") %>%
dyLegend(show = "always") %>%
dyEvent("2021-05-11", "Delta (VOC)", labelLoc = "bottom") %>%
dyEvent("2021-11-26", "Omicron (VOC)", labelLoc = "bottom") %>%
dyRangeSelector()
```
Hungary
=======================================================================
Row
-----------------------------------------------------------------------
### New cases
```{r, include=FALSE}
hun_covid_sub <- subset(hun_covid, select = -c(1:3, 5, 7:59))
hun_covid_sub$date <- ymd(hun_covid_sub$date)
str(hun_covid_sub)
data <- xts(x = hun_covid_sub$new_cases, order.by = hun_covid_sub$date)
names(data) <- c("New cases")
data <- abs(data$`New cases`)
```
```{r}
dygraph(data) %>%
dyOptions(fillGraph = TRUE, fillAlpha = 0.5, colors = "#337ab7") %>%
dyCrosshair(direction = "vertical") %>%
dyLegend(show = "always") %>%
dyEvent("2021-05-11", "Delta (VOC)", labelLoc = "bottom") %>%
dyEvent("2021-11-26", "Omicron (VOC)", labelLoc = "bottom") %>%
dyRangeSelector()
```
### New tests
```{r, include=FALSE}
hun_covid_sub <- subset(hun_covid, select = -c(1:3, 5, 27:59))
hun_covid_sub$date <- ymd(hun_covid_sub$date)
str(hun_covid_sub)
data <- xts(x = hun_covid_sub$new_tests, order.by = hun_covid_sub$date)
names(data) <- c("New tests")
```
```{r}
dygraph(data) %>%
dyOptions(fillGraph = TRUE, fillAlpha = 0.5, colors = "#337ab7") %>%
dyCrosshair(direction = "vertical") %>%
dyLegend(show = "always") %>%
dyEvent("2021-05-11", "Delta (VOC)", labelLoc = "bottom") %>%
dyEvent("2021-11-26", "Omicron (VOC)", labelLoc = "bottom") %>%
dyRangeSelector()
```
Row
-----------------------------------------------------------------------
### Hospital patients
```{r, include=FALSE}
hun_covid_sub <- subset(hun_covid, select = -c(1:3, 5, 21:59))
hun_covid_sub$date <- ymd(hun_covid_sub$date)
str(hun_covid_sub)
data <- xts(x = hun_covid_sub$hosp_patients, order.by = hun_covid_sub$date)
names(data) <- c("Hospital patients")
```
```{r}
dygraph(data) %>%
dyOptions(fillGraph = TRUE, fillAlpha = 0.5, colors = "#337ab7") %>%
dyCrosshair(direction = "vertical") %>%
dyLegend(show = "always") %>%
dyEvent("2021-05-11", "Delta (VOC)", labelLoc = "bottom") %>%
dyEvent("2021-11-26", "Omicron (VOC)", labelLoc = "bottom") %>%
dyRangeSelector()
```
### ICU patients (no data available)
```{r, include=FALSE}
hun_covid_sub <- subset(hun_covid, select = -c(1:3, 5, 19:59))
hun_covid_sub$date <- ymd(hun_covid_sub$date)
str(hun_covid_sub)
data <- xts(x = hun_covid_sub$icu_patients, order.by = hun_covid_sub$date)
names(data) <- c("ICU patients")
```
```{r}
dygraph(data) %>%
dyOptions(fillGraph = TRUE, fillAlpha = 0.5, colors = "#337ab7") %>%
dyCrosshair(direction = "vertical") %>%
dyLegend(show = "always") %>%
dyEvent("2021-05-11", "Delta (VOC)", labelLoc = "bottom") %>%
dyEvent("2021-11-26", "Omicron (VOC)", labelLoc = "bottom") %>%
dyRangeSelector()
```
### New deaths
```{r, include=FALSE}
hun_covid_sub <- subset(hun_covid, select = -c(1:3, 5, 10:59))
hun_covid_sub$date <- ymd(hun_covid_sub$date)
str(hun_covid_sub)
data <- xts(x = hun_covid_sub$new_deaths, order.by = hun_covid_sub$date)
names(data) <- c("New deaths")
```
```{r}
dygraph(data) %>%
dyOptions(fillGraph = TRUE, fillAlpha = 0.5, colors = "#337ab7") %>%
dyCrosshair(direction = "vertical") %>%
dyLegend(show = "always") %>%
dyEvent("2021-05-11", "Delta (VOC)", labelLoc = "bottom") %>%
dyEvent("2021-11-26", "Omicron (VOC)", labelLoc = "bottom") %>%
dyRangeSelector()
```
### New deaths per million
```{r, include=FALSE}
hun_covid_sub <- subset(hun_covid, select = -c(1:3, 5, 16:59))
hun_covid_sub$date <- ymd(hun_covid_sub$date)
str(hun_covid_sub)
data <- xts(x = hun_covid_sub$new_deaths_per_million, order.by = hun_covid_sub$date)
names(data) <- c("New deaths per million")
```
```{r}
dygraph(data) %>%
dyOptions(fillGraph = TRUE, fillAlpha = 0.5, colors = "#337ab7") %>%
dyCrosshair(direction = "vertical") %>%
dyLegend(show = "always") %>%
dyEvent("2021-05-11", "Delta (VOC)", labelLoc = "bottom") %>%
dyEvent("2021-11-26", "Omicron (VOC)", labelLoc = "bottom") %>%
dyRangeSelector()
```
Row
-----------------------------------------------------------------------
### People partially vaccinated (1st dose)
```{r, include=FALSE}
hun_vax$Date <- ymd(hun_vax$Date)
str(hun_vax)
data <- xts(x = hun_vax$People_partially_vaccinated, order.by = hun_vax$Date)
names(data) <- c("People partially vaccinated")
```
```{r}
dygraph(data) %>%
dyOptions(fillGraph = TRUE, fillAlpha = 0.5, colors = "#337ab7") %>%
dyCrosshair(direction = "vertical") %>%
dyLegend(show = "always") %>%
dyEvent("2021-05-11", "Delta (VOC)", labelLoc = "bottom") %>%
dyEvent("2021-11-26", "Omicron (VOC)", labelLoc = "bottom") %>%
dyRangeSelector()
```
### People fully vaccinated (2nd dose)
```{r, include=FALSE}
hun_vax$Date <- ymd(hun_vax$Date)
str(hun_vax)
data <- xts(x = hun_vax$People_fully_vaccinated, order.by = hun_vax$Date)
names(data) <- c("People fully vaccinated")
```
```{r}
dygraph(data) %>%
dyOptions(fillGraph = TRUE, fillAlpha = 0.5, colors = "#337ab7") %>%
dyCrosshair(direction = "vertical") %>%
dyLegend(show = "always") %>%
dyEvent("2021-05-11", "Delta (VOC)", labelLoc = "bottom") %>%
dyEvent("2021-11-26", "Omicron (VOC)", labelLoc = "bottom") %>%
dyRangeSelector()
```